Primer Design
AI Scientist includes 16+ professional primer design tools, accessible through the /primers command. These cover virtually all primer needs encountered in molecular biology research, from standard PCR to advanced mutagenesis strategies.
Primer Types
Section titled “Primer Types”| Primer Type | Description |
|---|---|
| Standard PCR Primers | Specify template and amplification region, auto-design forward/reverse primers |
| Gibson Assembly Primers | Automatically add 25-40bp overlaps for multi-fragment assembly |
| Site-Directed Mutagenesis | Design mutagenesis primers introducing specific point mutations |
| Saturation Mutagenesis (SSM) | Use degenerate codons (NNK/NNS) to cover all amino acid variants at target sites |
| Combinatorial Mutagenesis (COMBI) | Multi-site grouped combinatorial mutations for enzyme engineering |
| PAS Oligonucleotides | Large fragment/oligonucleotide library design |
| Sequencing Primers | Sequencing primer design with stepping coverage across the full sequence |
| Colony PCR Primers | Colony PCR primers for verifying transformants |
| SOE Primers | Splicing by Overlap Extension primer design |
| Insertion Primers | Primers for tag/linker insertion |
| Inverse PCR Primers | Outward-facing primers for vector linearization |
Quality Control
Section titled “Quality Control”Every primer designed by AI Scientist goes through automatic quality checks:
- Hairpin detection — identifies potential secondary structures that could reduce primer efficiency
- Dimer analysis — checks for self-dimers and cross-dimers between primer pairs
- GC clamp — verifies 3’ end stability for reliable annealing
- Tm matching — ensures forward and reverse primers have compatible melting temperatures
Batch Design
Section titled “Batch Design”For large-scale projects, AI Scientist supports batch primer campaigns. You can submit multiple targets at once, and the system will:
- Search your existing primer inventory for any previously designed primers that match
- Design new primers only for targets that lack coverage
- Consolidate all results into a single ordering table
Export
Section titled “Export”One-click export of primer ordering tables in CSV or TSV format, ready for direct submission to your oligo synthesis provider.